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[GUSDEV] Inserting Sequence Features - Problem with a big reference.
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From: Ricardo B. <rb...@gm...> - 2005-12-06 23:48:49
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Hi,
I am trying to load kinetoplastida_nt, using InsertSequenceFeatures
plugin. But I am not obtaining.
Kinetoplastida_nt has a register whose author field exceeds the maximum
size the table sres.reference.
How I must proceed to load this base?
It follows below the error:
[rbalbi1@crithidia bancos]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
$GUS_HOME/config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt
--fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
"2005-12-06" --commit
Tue Dec 6 21:32:42 2005 ARG algoinvo 1
Tue Dec 6 21:32:42 2005 ARG comment
Tue Dec 6 21:32:42 2005 ARG commit 1
Tue Dec 6 21:32:42 2005 ARG debug 0
Tue Dec 6 21:32:42 2005 ARG defaultOrganism
Tue Dec 6 21:32:42 2005 ARG extDbName Kinetoplastida_nt
Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06
Tue Dec 6 21:32:42 2005 ARG fileFormat genbank
Tue Dec 6 21:32:42 2005 ARG gff2GroupTag
Tue Dec 6 21:32:42 2005 ARG group
Tue Dec 6 21:32:42 2005 ARG gusconfigfile
/GUS/gus_home/config/gus.config
Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs
Tue Dec 6 21:32:42 2005 ARG help
Tue Dec 6 21:32:42 2005 ARG helpHTML
Tue Dec 6 21:32:42 2005 ARG inputFileExtension
Tue Dec 6 21:32:42 2005 ARG inputFileOrDir kinetoplastida_nt
Tue Dec 6 21:32:42 2005 ARG makeSourceids
Tue Dec 6 21:32:42 2005 ARG mapFile
/GUS/gus_home/config/genbank2gus.xml
Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass
Tue Dec 6 21:32:42 2005 ARG project
Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id
Tue Dec 6 21:32:42 2005 ARG seqSoTerm
Tue Dec 6 21:32:42 2005 ARG seqType
Tue Dec 6 21:32:42 2005 ARG soCvsVersion
Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0
Tue Dec 6 21:32:42 2005 ARG testNumber
Tue Dec 6 21:32:42 2005 ARG user
Tue Dec 6 21:32:42 2005 ARG verbose 0
Tue Dec 6 21:32:42 2005 ARG veryVerbose 0
Tue Dec 6 21:32:42 2005 AlgInvocationId 26
Tue Dec 6 21:32:42 2005 COMMIT commit on
Tue Dec 6 21:32:44 2005 Processing file 'kinetoplastida_nt'...
DBD::Pg::st execute failed: ERROR: value too long for type character
varying(1000)
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.Reference ( journal_or_book_name, group_write,
other_read, group_read, author, user_read, row_user_id, reference_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, title, user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, 1, 1,
El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., Aggarwal,G., Tran,
A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., Blandin,G., Westenberger,S.J.,
Caler,E., Cerqueira,G.C., Branche,C., Haas,B., Anupama,A., Arner,E.,
Aslund,L., Attipoe,P., Bontempi,E., Bringaud,F., Burton,P., Cadag,E.,
Campbell,D.A., Carrington,M., Crabtree,J., Darban,H., da Silveira,J.F., de
Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., Ferella,M.,
Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., Kindlund,E., Klingbeil,M.,
Kluge,S., Koo,H., Lacerda,D., Levin,M.J., Lorenzi,H., Louie,T., Machado,C.R=
.,
McCulloch,R., McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S.,
Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., Ramirez=
,
J.L., Rinta,J., Robertson,L., Salzberg,S.L., Sanchez,D.O., Seyler,A.,
Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., Tarleton,R.,
Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., Wickstead,B., Wortman,J.,
White,O., Fraser,C.M., Stuart,K.D. and Andersson,B., 1, 1, 6, 0, 26, 1, 1,
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease=
,
1 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d1=
4)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO SRes.Reference (
j...') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4=
d14)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY(0x8e82708)',
'\x{a} INSERT INTO SRes.Reference ( journal_or_book_name, grou...')
called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::Reference=3DHASH(=
0x987901c)',
'HASH(0x9889d48)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::Reference=3DHASH(0x987901c)=
')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
thanks,
Ricardo
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